Author: bugman
Date: Sun Mar 24 15:53:19 2013
New Revision: 19107
URL: http://svn.gna.org/viewcvs/relax?rev=19107&view=rev
Log:
Shifted the pipe_control.structure.superimpose module to
lib.structure.superimpose.
Added:
trunk/lib/structure/superimpose.py
- copied unchanged from r19105,
trunk/pipe_control/structure/superimpose.py
Removed:
trunk/pipe_control/structure/superimpose.py
Modified:
trunk/lib/structure/__init__.py
trunk/pipe_control/structure/__init__.py
trunk/pipe_control/structure/api_base.py
trunk/pipe_control/structure/main.py
trunk/target_functions/ens_pivot_finder.py
Modified: trunk/lib/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/__init__.py?rev=19107&r1=19106&r2=19107&view=diff
==============================================================================
--- trunk/lib/structure/__init__.py (original)
+++ trunk/lib/structure/__init__.py Sun Mar 24 15:53:19 2013
@@ -23,5 +23,6 @@
"""The relax-lib structure package - a library of functions handling
structural information."""
__all__ = [
- 'rotor'
+ 'rotor',
+ 'superimpose'
]
Modified: trunk/pipe_control/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/__init__.py?rev=19107&r1=19106&r2=19107&view=diff
==============================================================================
--- trunk/pipe_control/structure/__init__.py (original)
+++ trunk/pipe_control/structure/__init__.py Sun Mar 24 15:53:19 2013
@@ -35,14 +35,15 @@
independent of parser, writer, etc.
"""
-__all__ = [ 'api_base',
- 'cones',
- 'geometric',
- 'internal',
- 'main',
- 'mass',
- 'pdb_read',
- 'pdb_write',
- 'scientific',
- 'statistics',
- 'superimpose' ]
+__all__ = [
+ 'api_base',
+ 'cones',
+ 'geometric',
+ 'internal',
+ 'main',
+ 'mass',
+ 'pdb_read',
+ 'pdb_write',
+ 'scientific',
+ 'statistics'
+]
Modified: trunk/pipe_control/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/api_base.py?rev=19107&r1=19106&r2=19107&view=diff
==============================================================================
--- trunk/pipe_control/structure/api_base.py (original)
+++ trunk/pipe_control/structure/api_base.py Sun Mar 24 15:53:19 2013
@@ -37,7 +37,7 @@
# relax module import.
from data_store.relax_xml import fill_object_contents, object_to_xml,
xml_to_object
from lib.float import floatAsByteArray, packBytesAsPyFloat
-from pipe_control.structure.superimpose import kabsch
+from lib.structure.superimpose import kabsch
from lib.errors import RelaxError, RelaxFileError,
RelaxFromXMLNotEmptyError, RelaxImplementError
from lib.io import file_root
from lib.warnings import RelaxWarning
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=19107&r1=19106&r2=19107&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sun Mar 24 15:53:19 2013
@@ -38,7 +38,7 @@
from pipe_control.structure.internal import Internal
from pipe_control.structure.scientific import Scientific_data
from pipe_control.structure.statistics import atomic_rmsd
-from pipe_control.structure.superimpose import fit_to_first, fit_to_mean
+from lib.structure.superimpose import fit_to_first, fit_to_mean
from target_functions.ens_pivot_finder import Pivot_finder
from lib.errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError
from lib.io import get_file_path, open_write_file, write_data,
write_spin_data
Removed: trunk/pipe_control/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/superimpose.py?rev=19106&view=auto
==============================================================================
--- trunk/pipe_control/structure/superimpose.py (original)
+++ trunk/pipe_control/structure/superimpose.py (removed)
@@ -1,269 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2011-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module for handling all types of structural superimpositions."""
-
-# Python module imports.
-from copy import deepcopy
-from math import pi
-from numpy import diag, dot, eye, float64, outer, sign, transpose, zeros
-from numpy.linalg import det, norm, svd
-
-# relax module import.
-from pipe_control.structure.statistics import calc_mean_structure
-from lib.geometry.rotations import R_to_axis_angle, R_to_euler_zyz
-
-
-def find_centroid(coords):
- """Calculate the centroid of the structural coordinates.
-
- @keyword coord: The atomic coordinates.
- @type coord: numpy rank-2, Nx3 array
- @return: The centroid.
- @rtype: numpy rank-1, 3D array
- """
-
- # The sum.
- centroid = coords.sum(0) / coords.shape[0]
-
- # Return.
- return centroid
-
-
-def fit_to_first(models=None, coord=None, centroid=None):
- """Superimpose a set of structural models using the fit to first
algorithm.
-
- @keyword models: The list of models to superimpose.
- @type models: list of int
- @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
- @type coord: list of numpy rank-2, Nx3 arrays
- @keyword centroid: An alternative position of the centroid to allow for
different superpositions, for example of pivot point motions.
- @type centroid: list of float or numpy rank-1, 3D array
- @return: The lists of translation vectors, rotation matrices,
and rotation pivots.
- @rtype: list of numpy rank-1 3D arrays, list of numpy rank-2
3D arrays, list of numpy rank-1 3D arrays
- """
-
- # Print out.
- print("\nSuperimposition of structural models %s using the 'fit to
first' algorithm." % models)
-
- # Init (there is no transformation for the first model).
- T_list = [zeros(3, float64)]
- R_list = [eye(3, dtype=float64)]
- pivot_list = [zeros(3, float64)]
-
- # Loop over the ending models.
- for i in range(1, len(models)):
- # Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%models[i],
coord_from=coord[i], coord_to=coord[0], centroid=centroid)
-
- # Store the transforms.
- T_list.append(trans_vect)
- R_list.append(R)
- pivot_list.append(pivot)
-
- # Return the transform data.
- return T_list, R_list, pivot_list
-
-
-def fit_to_mean(models=None, coord=None, centroid=None, verbosity=1):
- """Superimpose a set of structural models using the fit to first
algorithm.
-
- @keyword models: The list of models to superimpose.
- @type models: list of int
- @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
- @type coord: list of numpy rank-2, Nx3 arrays
- @keyword centroid: An alternative position of the centroid to allow for
different superpositions, for example of pivot point motions.
- @type centroid: list of float or numpy rank-1, 3D array
- @keyword verbosity: The amount of information to print out. If 0,
nothing will be printed.
- @type verbosity: int
- @return: The lists of translation vectors, rotation matrices,
and rotation pivots.
- @rtype: list of numpy rank-1 3D arrays, list of numpy rank-2
3D arrays, list of numpy rank-1 3D arrays
- """
-
- # Print out.
- if verbosity:
- print("\nSuperimposition of structural models %s using the 'fit to
mean' algorithm." % models)
-
- # Duplicate the coordinates.
- orig_coord = deepcopy(coord)
-
- # Initialise the displacement lists.
- T_list = []
- R_list = []
- pivot_list = []
-
- # Initialise the mean structure.
- N = len(coord[0])
- mean = zeros((N, 3), float64)
-
- # Iterative fitting to mean.
- converged = False
- iter = 0
- while not converged:
- # Print out.
- if verbosity:
- print("\nIteration %i of the algorithm." % iter)
- print("%-10s%-25s%-25s" % ("Model", "Translation (Angstrom)",
"Rotation (deg)"))
-
- # Calculate the mean structure.
- calc_mean_structure(coord, mean)
-
- # Fit each model to the mean.
- converged = True
- for i in range(len(models)):
- # Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='mean', coord_from=coord[i],
coord_to=mean, centroid=centroid, verbosity=0)
-
- # Table printout.
- if verbosity:
- print("%-10i%25.3g%25.3g" % (i, trans_dist, (angle / 2.0 /
pi * 360.0)))
-
- # Shift the coordinates.
- for j in range(N):
- # Translate.
- coord[i][j] += trans_vect
-
- # The pivot to atom vector.
- coord[i][j] -= pivot
-
- # Rotation.
- coord[i][j] = dot(R, coord[i][j])
-
- # The new position.
- coord[i][j] += pivot
-
- # Convergence test.
- if trans_dist > 1e-10 or angle > 1e-10:
- converged = False
-
- # Increment the iteration number.
- iter += 1
-
- # Perform the fit once from the original coordinates to obtain the full
transforms.
- for i in range(len(models)):
- # Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[i], name_to='the mean structure',
coord_from=orig_coord[i], coord_to=mean, centroid=centroid, verbosity=0)
-
- # Store the transforms.
- T_list.append(trans_vect)
- R_list.append(R)
- pivot_list.append(pivot)
-
- # Return the transform data.
- return T_list, R_list, pivot_list
-
-
-def kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None,
centroid=None, verbosity=1):
- """Calculate the rotational and translational displacements between the
two given coordinate sets.
-
- This uses the U{Kabsch
algorithm<http://en.wikipedia.org/wiki/Kabsch_algorithm>}.
-
-
- @keyword name_from: The name of the starting structure, used for the
printouts.
- @type name_from: str
- @keyword name_to: The name of the ending structure, used for the
printouts.
- @type name_to: str
- @keyword coord_from: The list of atomic coordinates for the starting
structure.
- @type coord_from: numpy rank-2, Nx3 array
- @keyword coord_to: The list of atomic coordinates for the ending
structure.
- @type coord_to: numpy rank-2, Nx3 array
- @keyword centroid: An alternative position of the centroid, used
for studying pivoted systems.
- @type centroid: list of float or numpy rank-1, 3D array
- @return: The translation vector T, translation distance
d, rotation matrix R, rotation axis r, rotation angle theta, and the
rotational pivot defined as the centroid of the ending structure.
- @rtype: numpy rank-1 3D array, float, numpy rank-2 3D
array, numpy rank-1 3D array, float, numpy rank-1 3D array
- """
-
- # Calculate the centroids.
- if centroid != None:
- centroid_from = centroid
- centroid_to = centroid
- else:
- centroid_from = find_centroid(coord_from)
- centroid_to = find_centroid(coord_to)
-
- # The translation.
- trans_vect = centroid_to - centroid_from
- trans_dist = norm(trans_vect)
-
- # Calculate the rotation.
- R = kabsch_rotation(coord_from=coord_from, coord_to=coord_to,
centroid_from=centroid_from, centroid_to=centroid_to)
- axis, angle = R_to_axis_angle(R)
- a, b, g = R_to_euler_zyz(R)
-
- # Print out.
- if verbosity >= 1:
- print("\n\nCalculating the rotational and translational
displacements from %s to %s using the Kabsch algorithm.\n" % (name_from,
name_to))
- print("Start centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_from[0], centroid_from[1], centroid_from[2]))
- print("End centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_to[0], centroid_to[1], centroid_to[2]))
- print("Translation vector: [%20.15f, %20.15f, %20.15f]" %
(trans_vect[0], trans_vect[1], trans_vect[2]))
- print("Translation distance: %.15f" % trans_dist)
- print("Rotation matrix:")
- print(" [[%20.15f, %20.15f, %20.15f]" % (R[0, 0], R[0, 1], R[0,
2]))
- print(" [%20.15f, %20.15f, %20.15f]" % (R[1, 0], R[1, 1], R[1,
2]))
- print(" [%20.15f, %20.15f, %20.15f]]" % (R[2, 0], R[2, 1], R[2,
2]))
- print("Rotation axis: [%20.15f, %20.15f, %20.15f]" %
(axis[0], axis[1], axis[2]))
- print("Rotation euler angles: [%20.15f, %20.15f, %20.15f]" % (a,
b, g))
- print("Rotation angle (deg): %.15f" % (angle / 2.0 / pi * 360.0))
-
- # Return the data.
- return trans_vect, trans_dist, R, axis, angle, centroid_to
-
-
-def kabsch_rotation(coord_from=None, coord_to=None, centroid_from=None,
centroid_to=None):
- """Calculate the rotation via SVD.
-
- @keyword coord_from: The list of atomic coordinates for the starting
structure.
- @type coord_from: numpy rank-2, Nx3 array
- @keyword coord_to: The list of atomic coordinates for the ending
structure.
- @type coord_to: numpy rank-2, Nx3 array
- @keyword centroid_from: The starting centroid.
- @type centroid_from: numpy rank-1, 3D array
- @keyword centroid_to: The ending centroid.
- @type centroid_to: numpy rank-1, 3D array
- @return: The rotation matrix.
- @rtype: numpy rank-2, 3D array
- """
-
- # Initialise the covariance matrix A.
- A = zeros((3, 3), float64)
-
- # Loop over the atoms.
- for i in range(coord_from.shape[0]):
- # The positions shifted to the origin.
- orig_from = coord_from[i] - centroid_from
- orig_to = coord_to[i] - centroid_to
-
- # The outer product.
- A += outer(orig_from, orig_to)
-
- # SVD.
- U, S, V = svd(A)
-
- # The handedness of the covariance matrix.
- d = sign(det(A))
- D = diag([1, 1, d])
-
- # The rotation.
- R = dot(transpose(V), dot(D, transpose(U)))
-
- # Return the rotation.
- return R
Modified: trunk/target_functions/ens_pivot_finder.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/ens_pivot_finder.py?rev=19107&r1=19106&r2=19107&view=diff
==============================================================================
--- trunk/target_functions/ens_pivot_finder.py (original)
+++ trunk/target_functions/ens_pivot_finder.py Sun Mar 24 15:53:19 2013
@@ -27,7 +27,7 @@
# relax module import.
from pipe_control.structure.statistics import atomic_rmsd
-from pipe_control.structure.superimpose import fit_to_mean
+from lib.structure.superimpose import fit_to_mean
class Pivot_finder:
r19107 - in /trunk: lib/structure/ pipe_control/structure/ target_functions/